Contacts of the helix formed by residues 144 - 158 (chain R) in PDB entry 1G3I
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 144 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8R ARG* 4.7 0.7 - - - +
9R ASN* 6.5 1.6 - - - -
11R GLN* 6.4 1.8 - - - -
143R LEU* 1.3 74.3 - - - +
145R ALA* 1.3 65.5 + - - +
146R HIS* 2.8 10.6 + - - +
147R GLU* 2.8 48.6 + - - +
148R ILE* 2.9 18.5 + - - +
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Residues in contact with ALA 145 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6R VAL* 3.6 32.1 - - - +
8R ARG* 3.7 35.6 + - + +
11R GLN* 3.9 12.7 - - + +
13R VAL* 3.3 11.4 - - + +
143R LEU 3.5 3.3 + - - -
144R SER* 1.3 70.7 - - - +
146R HIS* 1.3 60.1 + - - +
148R ILE* 4.0 1.8 - - - -
149R VAL* 3.3 29.1 + - - +
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Residues in contact with HIS 146 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11R GLN* 5.7 0.2 - - - +
13R VAL* 3.4 21.0 - - + +
144R SER* 2.8 8.7 + - - +
145R ALA* 1.3 77.6 - - - +
147R GLU* 1.3 74.7 + - - +
149R VAL* 3.0 5.2 + - - +
150R GLU* 2.8 32.2 + - + +
169R ILE* 4.0 32.7 + - + +
171R GLU* 3.9 38.3 + - + +
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Residues in contact with GLU 147 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143R LEU* 3.3 31.6 - - + +
144R SER* 2.8 31.3 + - - +
146R HIS* 1.3 79.6 + - - +
148R ILE* 1.3 57.1 + - - +
150R GLU* 3.3 6.0 + - - +
151R LYS* 2.8 32.5 + - - +
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Residues in contact with ILE 148 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6R VAL* 3.6 23.1 - - + -
8R ARG* 4.4 2.9 - - - +
134R ALA* 4.0 7.2 - - - -
137R LEU* 3.7 21.3 - - + -
138R VAL* 3.1 44.6 - - + +
143R LEU* 3.7 29.4 - - + +
144R SER 2.9 18.5 + - - +
145R ALA* 4.0 4.7 - - - +
147R GLU* 1.3 76.3 - - - +
149R VAL* 1.3 56.1 + - - +
150R GLU 2.9 0.7 + - - -
151R LYS* 2.9 1.9 + - - +
152R SER* 2.6 47.1 + - - +
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Residues in contact with VAL 149 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4R VAL* 3.6 10.5 - - + +
5R SER* 4.0 6.3 - - - +
6R VAL* 3.2 39.7 - - + +
13R VAL* 4.1 9.2 - - + -
14R VAL 4.3 0.4 - - - -
15R GLY* 3.4 35.0 - - - +
145R ALA 3.3 16.9 + - - +
146R HIS 3.0 4.1 + - - +
148R ILE* 1.3 79.8 - - - +
150R GLU* 1.3 62.0 + - - +
152R SER* 4.4 5.6 - - - -
153R LEU* 3.2 20.1 + - - +
169R ILE* 4.0 11.9 - - + -
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Residues in contact with GLU 150 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146R HIS* 2.8 21.3 + - + +
147R GLU* 3.4 11.7 - - - +
149R VAL* 1.3 75.9 - - - +
151R LYS* 1.3 76.8 + - - +
153R LEU* 2.9 16.7 + - - +
154R ARG* 3.3 25.1 + - - -
167R PHE* 4.0 21.2 - - + -
169R ILE* 3.7 26.7 - - + -
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Residues in contact with LYS 151 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140L ASN* 4.7 12.8 - - - +
137R LEU* 4.0 17.9 - - + -
143R LEU* 5.9 2.2 - - + -
147R GLU 2.8 20.7 + - - +
148R ILE 3.6 2.2 - - - +
150R GLU* 1.3 81.3 + - - +
152R SER* 1.3 63.0 + - - +
154R ARG* 3.2 12.3 + - - +
155R ILE* 3.1 26.8 - - + +
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Residues in contact with SER 152 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4R VAL* 4.4 9.6 - - - -
130R ALA* 3.6 26.5 - - - -
133R ALA* 3.5 11.6 - - - +
134R ALA* 2.9 35.0 + - - +
137R LEU* 4.1 2.5 - - - +
148R ILE* 2.6 23.5 + - - +
149R VAL* 4.2 4.7 - - - -
151R LYS* 1.3 69.9 - - - +
153R LEU* 1.3 67.6 + - - +
155R ILE* 3.5 3.5 + - - +
156R ALA* 3.3 15.9 + - - +
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Residues in contact with LEU 153 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2R THR* 3.5 32.1 - - + +
4R VAL* 3.3 25.1 - - + +
15R GLY* 3.6 8.3 - - - +
16R GLY* 3.3 27.8 - - - +
17R ASP* 4.8 0.9 - - + +
130R ALA* 4.7 0.2 - - + -
149R VAL 3.2 17.2 + - - +
150R GLU 2.9 7.2 + - - +
152R SER* 1.3 78.5 - - - +
154R ARG* 1.3 63.8 + - - +
156R ALA* 3.1 6.3 + - - +
157R GLY* 2.8 19.9 + - - -
163R THR* 4.9 2.4 - - - +
167R PHE* 3.3 43.5 - - + -
169R ILE* 4.8 5.4 - - + -
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Residues in contact with ARG 154 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139L GLU* 6.0 2.2 - - - -
150R GLU* 3.3 21.5 + - - +
151R LYS* 3.2 13.8 + - - +
153R LEU* 1.3 76.7 - - - +
155R ILE* 1.3 73.3 + - + +
157R GLY* 2.8 15.6 + - - +
158R ASP* 3.1 26.2 + - - +
165R THR* 3.4 34.2 + - + +
167R PHE* 3.7 25.8 - - + -
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Residues in contact with ILE 155 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132L SER* 3.6 45.8 - - - +
135L ARG* 4.7 11.7 + - + +
136L ALA* 4.7 13.5 - - + +
139L GLU* 4.2 18.8 - - - +
140L ASN* 5.8 1.8 - - - +
129R TYR 4.7 1.8 - - - +
133R ALA* 4.1 17.3 - - + -
137R LEU* 6.4 0.7 - - + -
151R LYS* 3.1 22.4 + - + +
152R SER* 3.7 7.2 - - - +
154R ARG* 1.3 81.2 - - + +
156R ALA* 1.3 62.3 + - - +
158R ASP* 3.4 18.3 + - - +
159R ILE* 3.6 14.4 - - + +
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Residues in contact with ALA 156 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2R THR* 3.6 31.2 - - + +
126R GLY* 3.9 4.9 - - - +
129R TYR* 4.0 11.6 - - + -
130R ALA* 3.7 15.5 - - + +
152R SER 3.3 9.5 + - - +
153R LEU 3.1 8.5 + - - +
154R ARG 2.9 1.0 + - - -
155R ILE* 1.3 78.1 - - - +
157R GLY* 1.3 60.1 + - - +
159R ILE* 3.0 2.3 + - - +
160R CYS* 2.9 31.9 + - - +
163R THR* 4.3 1.6 - - - -
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Residues in contact with GLY 157 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G VAL* 6.0 0.2 - - - +
153R LEU 2.8 9.9 + - - -
154R ARG* 2.8 11.2 + - - -
156R ALA* 1.3 72.5 - - - +
158R ASP* 1.3 60.0 + - - +
159R ILE 3.1 1.1 + - - -
160R CYS 3.2 10.7 - - - +
163R THR* 3.1 42.4 - - - +
164R ASN* 4.4 8.1 - - - -
165R THR* 5.5 3.6 - - - -
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Residues in contact with ASP 158 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G VAL* 4.0 17.2 - - - +
135L ARG* 4.2 15.4 + - - +
154R ARG* 3.1 24.0 + - - +
155R ILE* 3.6 12.4 - - - +
156R ALA 3.1 0.8 - - - -
157R GLY* 1.3 76.8 - - - +
159R ILE* 1.3 64.2 + - + +
165R THR* 4.3 14.9 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il